Identity
by Karama9
Summary: ARAH continuity, so outside of my usual AU. Absolutely outside of it. A clone tries to come to terms with who or what he is, and with what defined his last life and this new one.
1. Chapter 1: The Clone

**Author's Notes**

Disclaimer: I don't own any of the characters or settings in this story. I'm just a fangirl. :)

This story is outside of my continuity, and was written for the sole purpose of getting it out of my head.

The setup is the newer issues of A Real American Hero. Spoiler ahead if you haven't read them.

Billy was killed by Cyber ninjas in issue 172, and Storm Shadow, for reasons I honestly can't explain, felt it was best to give the body to Cobra Commander. The fact Billy has a mother that never tried to kill him or brainwash him, and who is therefore easily argued to be the parent more deserving of having 'custody', or the fact that Billy would probably have hated the idea of his Cobra flag draped coffin being carried by siegies, never crossed his mind. The only glimmer of a logical explanation I could see came from Storm letting the Commander know Snake Eyes and himself would seek justice and telling him he could help by tracing the origin of the cyber ninja's technology; I figured Billy's body had been used to inflame the Commander and make him help in the hunt.

In the preview for issue 176 (I haven't read the full issue yet), Storm Shadow expresses surprise that the Commander is pissed enough to be violent about his search. There goes the 'make him mad with rage so he'll help' theory.

The cyber ninja story is still in full swing in the comics at the time of this writing, but this story is set a bit ahead, after that enemy has been dealt with (the assumption being that they will eventually be defeated). Continuity break: in the comics, Mindbender destroyed the Brainwave Scanner out of fear after the ghost of Venom tried to lure him inside the machine. I need the brainwave scanner for this story, so I decided that Mindbender did a very poor job of trashing it.

This isn't a light story. It's kind of existential and depicts someone dealing with a pretty major identity crisis.

One last note... in my usual continuity, I've strengthened the relationship between Tommy and Billy based on how they behaved before Billy's first 'death' and shortly after his return. For this story, I'm sticking closer to their fairly different characterization in the issues leading up to 172 and after. I'm still adding my own interpretation, obviously, but not as drastically as usual.

Many thanks to WillWrite4Fics and LadyJaye1 for their help and feedback on this story.

* * *

><p><strong>Identity<strong>

"Ah, Mindbender!" the Commander greeted. He gestured to a chair across his desk from his own. "Sit down, sit down. I have a project for you."

The doctor sat down warily. The Commander was acting far too courteously for his liking; past experience strongly suggested the man was about to request the impossible and that his mood would change completely once he was told as much.

"I would of course be delighted to be of service, Commander," he said. "What did you have in mind?"

"I've been thinking about Serpentor," the Commander said, leaning back in his chair casually, his fingers steepled in front of his chest. He was wearing his soft mask, and his eyes crinkled slightly when Mindbender winced.

"You know how much I regret this folly, Commander," Mindbender said. "If I may be so bold as to remind you that I've been punished already..."

"Yes, I would agree that burying you alive and causing your death was probably sufficient in terms of disciplinary action," the Commander said with a chuckle.

Mindbender swallowed. "Just the same, I am always eager for another chance to make it up to you, Commander."

The Commander waved the comment away. "I've also been thinking of you. You now have something in common with your creation, after all. You are both clones."

Mindbender had no answer to offer. The Commander was of course speaking the truth: his original body had died in the buried freighter, and he had been recreated along with his memories. He absolutely felt he was the real Mindbender, but there was no question that the body he inhabited was not his original one.

The Commander leaned forward and his eyes acquired a deadly serious expression. "You will clone Billy, and restore his memory and personality from the data you have in the brainwave scanner. I am guessing you don't have a ready to go 'backup' of him like you did for yourself, which is why I need you to do this. I'd be able to do it myself otherwise."

Mindbender swallowed; the demand would have been a relief if not for one small detail.

"I'm afraid the brainwave scanner is damaged beyond repair, Commander," he said softly, not meeting the man's eyes.

The Commander snorted. "For your sake, it better not be. You have a week."

Mindbender swallowed again, got up and bowed. "Yes, Commander."

* * *

><p>A week later, it was a very sleep deprived Mindbender who stood by the grown clone of the Commander's son. Despite the need to grow the body to adulthood and to reproduce the muscle tone and exact distribution of body fat, the physical recreation had been the easy part. The copy was not only perfect, but in better condition than the original thanks to missing neither an eye nor a leg.<p>

The difficult part, the part that had kept the doctor up for most of the last six nights, had been recovering the data from the damaged brainwave scanner and piecing it together to - hopefully - get a full image of the young man's psyche as of his last session in the scanner before Venom had started taking over. This implied figuring out when that take over had happened, and since it had been gradual, Mindbender had had to carefully analyze the thought patterns to determine when Venom's had started to not only be present but to dominate. Even physically repairing the scanner had been a breeze in comparison to that.

And all that effort was far from guaranteed to have worked. There was no way to tell whether there were holes in the recovered memories, and whether those holes would matter.

He held the pointer of his mouse hovering above the 'download' button for a long time before he gathered the nerves to click. The scanner immediately sprang to life with a loud humming sound, and sent the data to the currently inanimate flesh that would hopefully turn into a new version of William.

* * *

><p>Billy resisted the urge to groan when his thoughts started to clear from a deep sleep to wakefulness. He refused to give Cobra the satisfaction of showing pain or discomfort and beyond that, he preferred not to give any hint whatsoever that he wasn't in the state of euphoria the brainwave scanner victims usually woke up in. There was a slight possibility that the machine had misfired and that Mindbender would not know he was back to himself, after all.<p>

He opened his eyes and automatically lost his composure; both eyes had opened, and he was seeing out of both of them.

He sprang up and the way the visuals shifted confirmed his depth perception was back. He put his hand over his left eye anyway, for a final confirmation, and for a full minute, stared at the small cell he was in and at the lab beyond with his somehow restored right eye.

He stopped staring when he noticed Mindbender on the other side of the force field closing in his cell. The mad scientist was looking at him with an undecipherable expression.

"Who created this?" Billy asked, pointing at his eye. "Fred VII made this..."

He punched his right leg through the sheet covering it, expecting a metallic sound, and his eyes widened. What he had hit was soft, and he had felt the hit. He threw the cover off himself and jerked back with a yelp; he had an organic leg again, and he couldn't even see a scar where it would have been grafted.

He took a few deep breaths as he stared at his extremely natural looking and feeling limb.

"Okay, Fred VII didn't make THAT," he corrected himself. "Or is this just a cover over the old one? With nerve endings? But… why would…?"

He just didn't get it. That thing looked downright supernatural and had to have been insanely expensive to develop and create. And why? The metal one was working just fine, it didn't need replacing at all. Billy didn't picture his father spending millions in resources just so he'd look more natural wearing shorts. And why now, all of a sudden? As near as he could tell, he'd been working for the Commander, under the influence of the brainwave scanner, for months. Where was the ability to replace his eye and needlessly replace his leg suddenly coming from?

And why was the thought of the brainwave scanner not bothering him as much as it used to? That had to be a bad sign. It might mean he was getting addicted to it, somehow.

He turned to Mindbender and glared at him. "Explain," he demanded. "What is going on?"

Mindbender lifted his nose at him. "Short version? You're a clone. I've spent the last week creating you."

Billy's eyes widened. He could not detect any lie, and with Mindbender, that was a rarity. He also knew the doctor was a clone himself, the original having died in the freighter the Commander had trapped them in. As disturbing as it was, the clone theory also explained his restored eye and leg.

"I don't believe you," he said anyway. "If my father decided to make a copy of me, he wouldn't have you make me remember everything. He'd get you to only copy some very select memories. Heck, he'd probably get you to recreate me as a small child and just start over. And why would he bother with a copy when he can manipulate my mind in my real head anyway? And if I'm a clone, where's the real me?"

"The real Billy is dead," Mindbender said. "Storm Shadow killed him," he improvised. "Thus the need to create a copy."

"You're not that good a liar," Billy said, narrowing his eyes. "It's clear as day when you do it. Storm Shadow didn't…" he stopped and felt his pulse pick up.

Mindbender smiled nastily. "You can tell the lie, can you?" he asked. "Well then, surely you can tell the truths, as well. Billy IS dead. YOU are a clone… MY creation."

Billy glanced at his right forearm in desperation. A clone wouldn't have his tattoo. He felt his heart sink; his arm was bare. Closer examination also revealed his moles were gone as well. He performed the same visual test on his other limbs, and found them just as unnaturally devoid of any mark or scar.

He swallowed and frantically tried to assimilate the idea. A copy. He was a copy. Or his body was, at least. Mindbender obviously didn't consider himself anything less than the real article, perhaps he was right. His mind was intact, and that was the real him, wasn't it?

Except his 'mind' came from data files stored in the brainwave scanner. It was just as much a copy as his body. He was seized by a violent shudder and hugged his legs close to himself. He let go with a jerk; the right leg was all wrong. These weren't his legs, or his arms, or his body. The heart that was hammering in his chest wasn't his. The CHEST wasn't his.

But then again, it was. Wasn't it? This body did belong with his mind, both had been manufactured to work as a pair. The thought made him shiver again, and he cast his mind for something else, anything else, to focus on.

He was only partly successful. "I don't remember dying," he said. "Last thing I remember is telling Dad off for cancelling that mission…" He frowned. "I was going to be put back in the scanner. Are you saying the scanner killed me?"

"Don't be foolish!" Mindbender said angrily. "The scanner wouldn't have killed you unless I wanted it to. Your memories end where they do because I left out the later ones. Those were corrupted by Venom's thoughts, who was in the process of taking over your body. I couldn't revert back to before he started, I didn't have enough material, but you should find his 'presence' to be minimal at this point."

Billy could not hold back a groan this time and cradled his head in his hands. He forced his mind to focus on getting answers again. "Then how did I die?"

"Your father has instructed me to let him answer THAT line of questioning," Mindbender said. "For now, get up and walk. You need to get used to your body."

Billy raised an eyebrow; his cell allowed for taking maybe three steps.

Mindbender ignored his expression and left the lab. Billy clenched his jaw to resist asking him to stay; he was NOT that desperate for company. He wondered where Storm Shadow was and quickly decided he was hopefully far away from here. He didn't know how much time had passed since his last memories had been current, but if Venom had gradually taken him over, it had to mean it had taken at least a little while. Time enough for his former teacher to potentially escape, although come to think of it, he remembered months of time in which both of them and the Baroness had failed to do just that.

He sat up on the bed and got up carefully, testing his legs. The left one felt fine, but the right one felt weak and fragile in comparison to the titanium one he was now used to.

He scowled; he hadn't grown used to an artificial leg, he had never had one. He wasn't the same person he remembered being, he barely qualified as _a_ person.

He clenched his fists. That wasn't true. He WAS a person, he was himself. Past the superficial physical aspect, he had the exact same mind and up to a certain point in time, the exact same memories. He was just in a new body, and he might have to face a few words from narrow minded people. Mindbender was doing just fine with it all, so could he. He took another step, this time putting his weight on his new right leg. Or rather, on his right leg that was no newer than the left one; no newer than the rest of his body, including the head that was forming those thoughts and that was seriously beginning to throb.

* * *

><p>No less than twenty Crimson Guardsmen escorted him to the Cobra Commander's office. He'd been stewing in his cell for hours by then, and was fully aware that his father had arranged to make him wait on purpose.<p>

He pursed his lips; he really needed to stop thinking of the man as his father. The Commander's son was dead. But then again, he had the same genes he always had, so genetically speaking, he was just as linked to the Commander as ever.

He shook his head. It didn't matter; it wasn't like he wanted to be related to the Commander. His thoughts diverted to his mother. He'd talked to her several times since he'd taken off on her to try and find his father's murderer, and there was no question that they cared for one another, but they had both long since concluded that they were never going to have a traditional mother/son relationship. He didn't know how she'd react to him now.

He clenched his jaw and forced himself to focus on the more immediate concern of getting some answers. For all he knew, he'd been torturing himself for nothing; he'd thought about it quite a bit in his cell, and there was still a distinct possibility that he was not a clone at all, wasn't there? Occam's razor was his friend here, because Mindbender notwithstanding, clones were just not likely. And there could easily be another explanation for his eye and his leg, and his tattoo, and his moles, even if he couldn't really think of one at the moment.

The point was, there was definitely room for some reasonable doubt. Not reasonable enough to prevent him from spending most of his time accepting the idea he was indeed a clone, but most certainly enough to hope to be wrong.

The siegies stopped in front of an ornate door and knocked. Billy braced himself and willed his brains to concentrate and to stop delving on existentialist nonsense.

The Commander called out for him to be let in and the guards opened the door and walked in with him.

"Leave us;" the Commander said, not lifting his eyes from a document he was reading, "he won't harm me."

* * *

><p>The Commander waited while the guardsmen filed out. Billy's clone stood rigidly still, letting the men walk around him to get to the door and out, not taking his eyes, both his eyes, off him.<p>

He held the gaze, carefully controlling any outward sign of emotion. The last siegie closed the door behind him and the Commander allowed himself to relax a little; there was no benefit in appearing overly cold to the young – technically a mere day old – man before him.

This was a golden opportunity; his relationship with Billy had always been rocky at best, despite his best efforts to make his son see things his way. He could understand where the boy's reluctance came from, of course. A series of factors had contributed, from a misguided childish bout of temper that had led young Billy to run away, to various people - including that traitorous ninja Storm Shadow - filling the boy's head with their own ideas, to the Commander's own rash decision to sentence him to death along with Mindbender, Firefly, Fred VII and Zartan. He had regretted the decision within hours, but it was impossible by then to retract without losing the tenuous grip he was regaining on his organization. Billy had been guilty of the same crime as Fred VII in attempting to kill him, and not dealing the same punishment to both would have been a fatal show of weakness.

These things were all in the past, however, and the Commander had truly enjoyed the time Billy had spent under the influence of the brainwave scanner, purged of the moral codes and ideas drilled into him for most of his life. It had been a huge disappointment to lose him to the ninjas again, and his death had been like a slap in the face. He was being denied any chance of ever making his son share his views and ambitions again and by delivering the body, Storm Shadow and Snake Eyes had further emphasized the fact that the boy had been theirs in the end. He'd set out not only to avenge his loss but also to deprive the ninjas of the satisfaction of exterminating the murderers themselves. Complications had robbed him of a complete victory in that regard.

Still, the elimination of the cyber ninjas had helped clear his mind, and the result of that new clarity now stood before him. This clone was raw potential; he could be the son the Commander had never had. Whether he would live to that potential was what the Commander now intended to find out. He would do his very best to make things clear to Mindbender's latest creation, and if the young man was able to choose the best path for himself, with no influence from the brainwave scanner, he would finally have a son that could be his pride and his heir and not be at risk of reverting back to a different temperament. Otherwise, the experiment would be classified a failure and the creature destroyed.

He got up, walked to the clone, and embraced him. He needed to show him that he could be loved and accepted.

True to the original, the creature that no doubt thought of itself as Billy did not return the hug. He did not push away either, however. The Commander saw it as a good sign; it showed confusion, uncertainty, and a confused mind would be much easier to turn to his side.

The Commander broke the hug but kept his hands on the clone's shoulders. "Mindbender tells me he's already explained what you are. Do you still have any doubt that what he's told you was the truth?"

He avoided being specific; he preferred not to use any labels yet, allow the clone to pick up on the fact who and what he was to him was still to be determined. He was very well prepared for this conversation, every last one of the lines he planned to say, every move he planned to make, all carefully studied to have the best effect. Even the videos he intended to show the clone had been picked because they were the ones he still couldn't watch impassively himself; the clone would witness genuine reactions. All part of the performance meant to naturally influence this new Billy into embracing a life assisting his father.

If he failed in his attempt, despite his best efforts, he'd at least have the satisfaction of killing the little traitor himself this time.

* * *

><p>Billy forced himself to keep his composure; the Commander was avoiding coming right out and calling him a clone. The part of him that still hoped Mindbender had been lying through his teeth automatically thought his father was avoiding an explicit lie, but the more rational part of him recognized the tone and mannerism as purely manipulative.<p>

"I remember everything," he said in lieu of a direct answer. "From my early childhood, up to when I was angry because you cancelled that mission. Every last one of those memories feels real; they don't feel like they belong to someone else."

"No, they wouldn't," the Commander said patiently. "We could implant you with the memories of a random stranger and they'd feel like yours too. Memories are in the first person, they always feel real. But obviously, the answer to my question is yes. That's not surprising… in fact, I suspected you would."

Billy hid his annoyance at the 'good loving father' act. "Can you prove it?" he asked. "Can you prove the 'real' me is dead and that I'm a copy?"

Instead of answering directly, the Commander took a remote control from his desk and pointed it at a screen to his right. The screen flickered briefly and a video started playing.

Billy felt his stomach lurch: it was an autopsy, and despite the missing eye patch and most of the titanium leg having been severed, despite the shredded mess that had replaced half of his midsection, there was no mistaking the corpse. That was him; he was watching his own autopsy.

He wasn't conscious of moving towards a chair but he collapsed on one anyway, his breathing short and feeling stomach sick, but completely unable to look away.

The doctors performing the autopsy did their thing, opening him up in several places in the process, poking and probing and doing Billy didn't know what, and eventually reported that several vital organs had been cut open, causing poisoning, acidic burn and internal bleeding in addition to the massive blood loss from the external wound itself. They estimated that death had probably occurred within a minute of the wound being inflicted.

The video cut then, and Billy forced his breathing to slow into deep breaths. He refused to pass out.

"Do you think this could be a fake?" the Commander asked.

Billy shook his head, defeated. He noticed his vision blurring and irritably wiped at his eyes. His two brand spanking new, laboratory-grown eyes. He would have loved to think the autopsy was an elaborate fake, but he knew it wasn't. It was too realistic, and perhaps even more importantly, the Commander had been visibly angry while watching it, even through his attempt at appearing grief-stricken instead.

"The people responsible were cybernetic ninjas who had a grudge against the Arashikage," the Commander said. "We've wiped them out of existence."

Billy's eyes widened. "Did they kill anyone else?" he asked.

The Commander shook his head. "They killed a lot of people, including many of my men, but I'm guessing your concern is limited to your ninja friends? They all live."

Billy nodded to acknowledge the answer, but could find nothing to say.

"Billy was with Storm Shadow and Snake Eyes when the murder happened," the Commander started.

"Both?" Billy asked, cutting him off. "Were we all free, or all your slaves?"

The Commander snarled in what was doubtless meant to pass as righteous anger. "Slaves?" he hissed. "I never enslaved any of them! I freed them from their self-imposed chains!"

"Fine!" Billy snapped, his patience rapidly evaporating. "Whatever you want to call it, were we under the influence of the brainwave scanner or not?"

"No," the Commander replied, still snarling. He took a big breath before he continued in a calmer tone. "Back on subject, I'm afraid I have very little information on the incident. Storm Shadow did not give me any details on what happened when he brought me the body."

Billy's brow furrowed. He knew he was reacting exactly as the Commander wanted him to, but he couldn't help it. "He… he brought you my body?"

The Commander nodded soberly. "He did at least that much right, yes. Thankfully, since it allowed me to at least properly say goodbye." He pointed the remote control at the screen again, starting another video. "I assume you're curious, perhaps even worried I may have somehow been disrespectful. This will hopefully put your mind to rest."

Billy once again found himself unable to look away; this video was of his funeral. He felt sick to his stomach again, though for different reasons. The video was thankfully short, and when it cut out, he levelled a glare at his father.

"You know damn well this is pretty much the last thing I would have wanted!" he said, his tone rising. "Siegies carrying me? In uniforms? And a Cobra flag draped on my coffin? Which part of this do you figure WASN'T disrespectful?"

The Commander looked away. "I was hoping you'd forgive a father's coping mechanism," he said. "What else would you have expected? I spent the last few years desperately wishing for my son to be a part of my life again, to take his place at my side!"

Billy's nostrils flared and he had to resist rolling his eyes at the melodramatic tone, but he had to admit the Commander had a point; his actions were not surprising in any way.

"Storm Shadow bringing the corpse here and giving me some of the technology used by the cyber ninjas also allowed me to track the murdering scum down and avenge my son's death," the Commander continued. "I assume that's why he did it, especially since he all but asked for my assistance."

Billy's eyes widened. "He… sought revenge too?" he asked. "And he allied himself with you for it?"

* * *

><p>The Commander paused. That had not been the expected answer at all. He opted to try and make his point – namely, that after failing to keep him alive, the ninja had used Billy's body as a tool to secure Cobra's assistance - again.<p>

"He said Snake Eyes and himself were honour bound to seek justice. They obviously hoped that if I shared their grief, I would share their quest… and to ensure that I was incensed enough for their purpose, they left my only child at the foot of my bed, mangled and lifeless."

Billy's eyes narrowed. "You can stop trying to make me angry with Storm Shadow. Rest assured that I am."

The Commander held the gaze. He should have known the little pest would throw off his script no matter how much he tried to account for every possibility.

"I am merely trying to let you know the facts," he said. "Don't you know why I had Mindbender create you?"

This at least put him back in control. The clone's eyes widened again and he sighed.

"No," he admitted. "From the way you talk, it's quite obvious you don't think of me as Billy. And if you just wanted an agent, you would have manipulated my memories to ensure my loyalty."

"You are still my flesh and blood," the Commander said, leaning over him. "But I don't want my relationship with my second born to be dependent on a machine. Think carefully, son. Do you really think my wanting to fix this World makes me a monster?" He sighed, back on script. It was time for the short speech he had practiced for nearly an hour in order to make sure he sounded sincere. "Losing Billy has opened my eyes. I see now that I strayed somewhere along the way; Cobra became less about helping the little guy and more about taking back the power. I should never have allowed myself to become so unaware of what was going on in the rest of the World. I blame myself for the existence of the cyber ninjas… I know about ninjas, I know this level of technology exists, I should have been watching more carefully. Helping the common man should not be limited to defending him against the government."

He grabbed the clone's upper arms. "Help me," he pleaded. "Be by my side as Billy was meant to be. Keep me on the right path, and together, we will make things right."

The clone tilted his head. "You want my help? You'd… listen to me?" His eyes started to look suspiciously shiny. "Turn things around? And… what did you just call me?"

The Commander pulled him up into a hug. He had time to think that the clone hadn't been as hard to manipulate as he'd feared before he felt a flash of pain on his neck and everything went black.

Unsurprisingly, the failed experiment was gone when he came to.

* * *

><p>Three days later, Billy found himself in front of a very familiar building in New York.<p>

Escaping from Cobra hadn't improved his situation all that much; he was just as lost as he'd been since waking up. He felt like he was himself but knew he wasn't; he knew he was no different than he'd been but then knew he was a mere copy.

It was maddening. He hadn't even slept since he'd found out what he was. He supposed that meant he had never fallen asleep, period. He didn't know whether he even could; it was possible that part of him was defective. He figured he wouldn't know for sure until he passed out from sheer exhaustion or outright died - assuming he could die. He didn't know THAT, either, not for sure.

He didn't even know why he had come here. And yet, he found himself taking the elevator to the rooftop. He stayed at the edge of the access door a while, staring at the water tower.

Storm Shadow could not help him; not this time. And why would he? He had no obligation to a clone. Billy wasn't even sure why the ninja had kept welcoming him back. He of course appreciated it, but he still kept leaving.

He started mentally reminding himself that he had technically never even met Storm Shadow, but stopped and sighed. He was sick of correcting himself like that. It was exhausting, and it was pointless; he couldn't help it, his memories were far too clear not to think of them as his.

And the Commander, who had arranged for him to remember all those things, had thought he'd make him believe he was meant to be a new son, a second born of sorts, and that he could take the place the eldest had left vacant. Perhaps the man even believed it himself, but it was still a load of crap. He wouldn't have restored all of Billy's memories into him if he'd wanted a different individual.

The thought brought his mind back to the other things he had learned from his conversation with the Commander. Namely, of what his former teacher had done. He felt the blood rush to his head and his upper lip curl. That alone made it worth seeking out Storm Shadow; the ninja had some explaining to do about what he'd done with his corpse.

_The_ corpse, he mentally corrected before he could help himself. Not _his_ corpse; he didn't have one. His body was still alive, and he had no actual right to be angry because Tommy hadn't done anything to him. He cursed and started walking towards the tower. If nothing else, it'd be a good place to think and maybe figure out his next step. Besides, what were the odds of Storm Shadow even being there?

He detected the presence in the tower just before opening the trap door and froze on the ladder. He knew enough to guess there was an arrow pointed straight at his heart right now.

"It's…" he stopped. He'd been about to say 'it's me', which was not exactly true and which would not have reassured the man in the tower any.

"Can I come in?" he asked instead.

And then rolled his eyes at himself. He was still alive, wasn't he? He opened the trap door and climbed in with his hands held high and wide apart.

Storm Shadow kept his arrow pointed at him, his expression unreadable. Billy swallowed and forced himself to look the man in the eyes. He hadn't thought things through very well; how else was Tommy going to react upon seeing him? For all his former teacher knew, he was a Cobra agent made to look like his protégé.

"I…" he started.

Tommy interrupted him. "Were you implanted with Billy's memories? Like the new Mindbender was with the old's?" he asked.

Billy nodded. "Da… the Commander didn't even manipulate them. Or I don't think he did, anyway. Mindbender says he cut them short, though, because Venom was somehow possessing m… Billy at one point. He's already a bit in here, actually." He pointed at his head. "I haven't noticed anything off, though, except I'm not afraid of the scanner. That's got to be Venom's influence because I've always been terrified of the thing."

Storm Shadow's expression had gradually been shifting towards pity as Billy was talking, and he suddenly lowered his bow. Billy blinked, wondering what he'd said that was so convincing.

"You said you've always been terrified of the scanner," Tommy said in answer to the unspoken question. His voice matched his expression. "And you only just caught yourself twice before that. You feel like you're him, don't you?"

"I know I'm just a copy."

Tommy pondered that for a moment, then nodded. He sat, deposited his bow next to him and gestured at his guest to sit down as well.

Billy sat and, more to break eye contact than anything else, looked around the familiar room. His eyes fell on a row of framed pictures. He had seen some of them before and knew they were clan members who had passed on. He'd actually met two of the people pictured. His eyes widened when they got to the end of the row; the last picture was of himself. He felt his blood boil again as he suddenly remembered what he'd wanted to talk to the ninja about. He levelled a glare at the other man.

"How COULD you?" he asked, his upper lip curling in a snarl and his eyes, maddeningly, threatening to flood. "If I'm part of the clan, how DARED you give my body to the Commander? Didn't you know what he'd do? He even draped the coffin in a Cobra flag!"

Tommy winced and acquired a pained expression. "I am sorry," he said. "I'm not quite sure what I was thinking... Psyche Out believes I fell back on abstract notions of honour and on protocols as a way to shut down emotions I could not afford because of the situation; grief of course, but mostly guilt."

Billy felt his anger towards his former teacher melt away. The apology was obviously sincere, and beyond what Psyche Out thought, there was another big sign he'd already caught on that showed the ninja had not quite been in his right mind.

"You fell back on protocols, all right," he said. "Do you realize what you did? Seeking justice? Telling my… the Commander how he could help?"

Tommy nodded. "I followed the exact same behaviour as when the Hard Master was killed. After all this time and effort trying to break the circle of vengeance I was caught in for so long, I simply called it justice instead and plunged right back in. And I allied myself, or tried to, with the very same evil as before. This time with less excuse because unlike when the Hard Master died, I was not alone, I had allies to help me." He sighed heavily and then, incongruously, chuckled slightly. "It turns out Snake Eyes is terrible at keeping me sane."

"How did I end up with the two of you? Did he rescue us? But how did he get us back to…" he stopped mid-sentence, realizing he was talking as if he were Billy again, and cursed. "I'm sorry. I bet this is really disturbing."

"Even more for you than for me, I'd say."

Billy sighed. "Yeah. I remember everything. Or I think I do, anyway," he added, cradling his head. "It feels like it was all me. But I KNOW it wasn't. But I don't know if it really makes a difference. I honestly think I'm the same person. I mean, no, I don't, I know I'm not, I'm not even… but…" he trailed off and sagged, head down. "I can't figure it out."

"You're you," Storm Shadow said. "Whether that's the Billy from the memories you were given, or a new person, is ultimately up to you."

Billy rolled his eyes. "Don't be ridiculous, it's NOT." He pointed at the pictures on the wall. "I know those are there to honour the spirits of the fallen. How can you tell me I can decide to be Billy? I'm just a copy! Real people have souls; I'm pretty sure I don't, unless you count the one that was programmed in! And I'm damn sure I don't have HIS soul!" he finished, pointing at his own portrait.

"You're _sure_ of it? Really? You're a step ahead of me, then."

Billy frowned. "What?"

"I think your emotions indicate that you do have a soul," Storm Shadow said. "I have no idea how that is, but it seems to me that the idea of Billy's spirit choosing to return to a new body is not that much more far fetched than the idea of a soul being created by a machine."

Billy literally felt his jaw drop.

"I'm not saying that's what happened," Storm Shadow specified. "What I'm saying is that it's up to you to decide what to believe. You can't control what others will think, but you can at least choose your own truth."

"And what do YOU think?" Billy asked. He pointed at his portrait. "Are you going to take that down?"

Tommy took a moment to consider, but eventually broke eye contact, looking down, and shook his head. "Not unless you stay for a while and it bothers you too much."

"Not buying the reincarnation theory after all, huh?" Billy sneered.

"Billy died in my arms," Storm Shadow replied. "Too quickly to say anything, or to hear anything I said."

The clone sighed and shook his head in disgust. It wasn't a proper answer to the question at all, and yet it explained the ninja's take on things quite well and so, sort of did answer the question.

"What DID you say?" he asked.

Storm Shadow looked for a moment as though he was not going to answer. Billy could guess his old mentor was tempted to point out that it had been private. "I just wished him serenity in the next life," he finally said.

The clone snorted. "So you don't WANT me to be him. Can't blame you."

"Of course I wouldn't wish your predicament on him; I wouldn't wish it on anyone. Least of all you."

"You mean him," Billy corrected automatically.

"No, I mean both of you. I can't think of you as Billy, but part of me will never be certain I'm not making a mistake on that. And also…" he trailed off and sighed. "And also, you are at the very least a living memory. There is a strong connection between the two of you, and…" Another sigh. "Billy was my responsibility and I failed him. I can't make it up to him but you, I may be able to help."

"And how do you plan on doing that? I don't need help, I just need to get a grip and move on."

"Swallow your pride," Storm Shadow lectured. "You're rightfully confused and distressed. Discipline, hard work and meditation could help you focus, organize your mind and find yourself. I can provide the guidance of a teacher and the support of a friend."

Billy made a face. "Friend? What if I feel like I AM Billy? You obviously don't."

"Differences of opinion," Storm Shadow said with a shrug. "I would not try to impose mine."

The clone snorted. "Yeah, right. You already said you weren't taking the picture down. And you're going to call me Billy, are you?"

"I said I'd take it down if you stayed and it really bothered you. As for your name…" he hesitated. "Would you settle for William?"

The clone did not answer right away. The offer was certainly more tempting than leaving and finding himself with no idea where to go or what to do again, like he had when he'd escaped Cobra. And truth be told, the tower did feel like home. He supposed that maybe that wasn't too surprising; he'd lived here, or Billy had, for longer than most any other place.

The question was, would home help? What if it influenced him into deciding who to be by making him nostalgic for who he remembered being? But then, with Storm Shadow treating him like someone new, and with that damn portrait, he'd hardly be able to delude himself into thinking that everything was as it had been.

It really was tempting. It felt like an opportunity to start over, to start fresh.

"Is there really that much more you can teach me?" he asked. "I remember everything I've already learned."

"I'm guessing your muscles don't," Storm Shadow said, "and you will probably find that the mind training has a very different feel now. It always does when you do it again after life changing events."

"Don't you have to go back to the Pit soon? What are you even doing here now?"

Storm Shadow smirked. "Going on a private vendetta and visiting the Cobra Commander without capturing him failed to impress Hawk. Psyche Out's professional opinion is that my actions were the result of shock and grief and recommended medical leave. As for when I should report for duty, I'll make arrangements. Don't worry about it."

"William will do," the clone said, offering his hand to his once more mentor, "and you can leave the picture. Thank you."

Tommy shook the offered hand and nodded. "Welcome home, William."

Fin


	2. Chapter 2: Last Word

**Author's Notes**

I know I had marked this as complete. I'm sorry. This plot bunny was very demanding, and I felt it belonged here since it is in fact a continuation of the previous chapter. I'm now marking this story as in progress, because it is in fact possible that I'll keep revisiting this setup. For one thing, I'm told that I should follow Tommy through at least part of what he says he's about to do at the end of this chapter.

Thanks to everyone who provided advanced feedback on this!

* * *

><p><strong>Chapter 2: Last Word<strong>

"I've been thinking."

Tommy stopped, a bite of fish halfway to his lips, and looked at the young man seated across from him.

William's hands were on his thighs and his plate sat ignored on the low table. The brown eyes were fixed on the ninja master's own; two eyes blazing out of the face of a dead b... man. Billy had been a man by the time he had died, not a boy; no matter how stubbornly his teacher's brains insisted in picturing him as a child.

His new protégé, however, he did not picture as a boy. Given that William was less than two weeks old, this was perhaps a bit ironic. Maybe it was a defence mechanism; maybe his heart was finding ways to disassociate the clone from Billy so as not to get too attached. Goodness knew he could not rely on his sight to accomplish this distinction; thanks to both his eyes being intact, William looked even more like the boy Storm Shadow had broken out of Cobra's dungeons than Billy himself had by the time he had been killed.

"What about?" Tommy asked. He resisted the easy jokes on the level of danger inherent to his student's thinking; it was obvious from the young man's expression that this was important to him.

"That bit yesterday about falling back on protocols. I don't buy it."

Tommy frowned. "You pointed out yourself that I fell into the exact same behaviour pattern as when my uncle was killed."

William nodded. "I know that. And you did. But that's not why you brought the body to the Commander. IF it was, you would have brought it to my...to Billy's mom. She's the one you trusted to care of him, not his dad. If the Commander had ever burst into your dojo, you would _never_ have let me… I mean Billy, leave with him! But you brought him the body. Why?"

Storm Shadow clenched his teeth and lowered his eyes. He noticed he was still holding his bite of fish and deposited it, along with his chopsticks, back on his plate. William was of course right, although the ninja had hoped to get away without having this conversation.

"Can't you guess?" he asked. There was some bitterness in his voice that he hadn't intended to let in there.

"Nope. It doesn't make any sense to me. The Commander told me you wanted to make him angry enough to join in the hunt against the cyber ninjas, but I know you wouldn't have used m.. Billy's body like that. But I have no clue why else you would do that!"

Storm Shadow snorted. William noticed his teacher's upper lip had curled up, just a little, into the beginning of a snarl.

"My next theory was that maybe you thought that's what Billy would have wanted, but..." the clone scratched his head. In order to believe that, Storm Shadow would have had to be seriously delusional, or remarkably stupid.

"But what?" Storm Shadow was frowning at him, now. Obviously, this topic was a very sore spot for him.

"But there's no way you'd think that," William finished. "You would have known better."

"I thought I did," Tommy said. He noticed his voice was almost a growl and forced himself to take a deep breath before he continued. "I caught Billy and held him as he died, convinced that I was at least providing some comfort by being there." He snorted. "I always did have a tendency to think too highly of myself."

William frowned; it was his turn to be confused. Storm Shadow sounded as though he'd been given reason to believe Billy had not wanted his presence. Even if he had no memory of the events in question or of the few weeks before then, the clone felt pretty certain that wasn't possible; he couldn't think of anyone else he'd be seeking out if he were dying. He didn't get a chance to voice his opinion: his teacher started talking again after only the briefest of pauses.

"So; if it wasn't because of protocols and it wasn't strategy, why else do you think I might have brought Billy's body back to the Commander?" The ninja's voice sounded bitter again. "It was a mistake; I shouldn't have listened, I should have realized he'd regret the requ…"

"He asked you to?" William cried out. He refused to believe it; unless the brainwash had had some serious lingering side effects, he would _never_ have made such a request. "Wait... you said yesterday he didn't have time to say anything."

Storm Shadow nodded, his face set in a stony expression that failed to hide the storm underneath. "I lied; I was trying to avoid this conversation. I still don't understand why we even need to have it. You have all his memories so again, can't you guess what he said and why?" He sighed. "I didn't lie _much_. He grabbed my arm, very weakly, and asked for his father. His dying request, one he could only manage to utter with one short word, was for his father."

Tommy stopped and took a deep breath. The request had broken his heart; he had tried to provide his protégé with a new family but in the end, he had failed. Despite everything, it was his father that Billy had cried out for as he died. The father who had tortured him, attempted to kill him by burying him alive and brainwashed him had held on to the boy's heart through it all, had retained the power to hurt him and had denied him the ability to make a new home and a new life for himself.

His eyes flew open when he heard William groan. He frowned at Billy's clone, irritated at the young man for the reaction which could only serve to prolong the conversation. His scowl was met with a disgusted expression.

William sighed, shook his head and rolled his eyes all at once. "I could slap you right now," he said with a slight snarl. "Well, okay, no; I couldn't. But I could try. How much of an ungrateful brat do you think I was?"

Tommy's scowl deepened. "It's not a matter of being ungrateful. He just…"

"…still loved the Cobra Commander like a father? No he didn't. I can guarantee you that."

"Something that happened in the weeks you are missing must have…"

"No, it didn't. It couldn't have. Look..." He trailed off, unsure how to broach the subject. He had never really found a way to talk about this, had he? That was part of the issue. It wasn't even a matter of being honest; he just didn't know how to say what he meant. He decided to try and get to it through what had actually happened; hopefully, actual events would be clearer than abstract concepts. "He only managed the one word, right? Father, wasn't it? Not Dad."

Tommy nodded. "I can't explain why it's so surprising to you, but whatever the reason is..."

"It's not surprising at all. I would have done the same thing."

Storm Shadow frowned again, the expression a mixture of puzzlement and growing anger. "Then what..."

William cut him off. "And I know what I would have meant, so I know what HE meant. He wasn't asking for the Commander, you idiot! He meant YOU!"

Tommy's eyes widened and he felt his jaw drop slightly. He clenched his jaw shut again and scowled at William. "I don't think so. Billy knew that we considered him family, but he never gave any indication that..."

William rolled his eyes. "I KNOW that!" he cried out, throwing his arms wide. "Because it's complicated! I don't... look, I'm not saying he meant it literally." He felt himself turn a bit red and decided to ignore it and just keep talking. It was time to come clear, heck it was obviously past time. "Of course he didn't mean it literally. But if it was me dying, and I had time to say something and you were right there, I... I'd try to thank you. Because even if you're technically more of a big brother, you're still the closest thing I ever had to a father. You're the only person who raised me at all since the Commander took me away from my mom, and each time I leave and come back, you're still there for me. And if I was dying and I didn't have time to say all that, or figure out where to even start, I'd still try. And that's what Billy did. He held on to you and muttered 'father' to tell you that if he could have picked his dad, it would have been you. He couldn't, he was stuck with the Commander, but the Commander is just… dad. He's no father."

Tommy took a few deep breaths, trying to assimilate the idea. He wasn't sure whether he believed it or not, and he was even less sure of whether he _wanted_ to believe it. On one hand, Billy had written something very similar when he'd left to go confront his father. It also made more sense than the thought his protégé really wanted to be reunited with the man he had just escaped. On the other hand, Billy had not acted as though he still felt that way in recent years. But then, reasonably, how would he have? He sighed and massaged his temples. He couldn't even begin to guess what had been in his student's mind, but William knew for a fact everything that had been there just a few weeks before Billy's death.

"Are you sure about this?" he asked the clone. "Absolutely sure? This is important, think about it carefully."

William did, as much as he could; it was a lot like asking someone to think about it carefully before confirming that the sky is blue. "Totally sure," he replied after a moment. "Why?" he added. The slight snarl was back. "Kind of late to do anything about it, isn't it?"

Storm Shadow got up. "Late yes, but not TOO late. I cannot undo what's happened, but I can make it right. I'll be back sometimes tonight, maybe early tomorrow."

William blinked at the ninja, who was already opening the trap door. "You're going to recover the body and do the Arashikage rituals?" he asked. He could hardly believe it and maddeningly, he found himself tearing up.

Tommy looked back at him as he went down the ladder. "It's what I would have done in the first place had I not believed he wished otherwise. I won't let the mistake stand if I can help it."

The trap door closed.

William swallowed the lump in his throat. "Thank you," he muttered at the intention of his mentor. He swallowed again and turned to Billy's portrait. "And _you_'re welcome."

**Fin**


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